Additional file 3 of A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference

Additional file 3 : Figure S1. Quality scores and accuracy of Illumina Hiseq 100-bp paired end reads for H. caudiculatum and H. dentatum after quality filters. Bad quality reads that showed values 20 on the histogram were discarded. All reads above the value of 30 indicates 99.9% of accuracy, regarding to bases correctly read by the sequencer, Figure S2. Training progress of the average distances of genes of H. caudiculatum and H. dentatum using Self-Organizing Maps showing the effect of neighborhood shrinking to include the winning unit, i.e., when the vectors in the dataset reach the closest similarity. Figure S3. Codebbook vectors for H. caudiculatum and H. dentatum showing the clusters of differentially expresed genes with maximum neighbouring after training process. The codebook vectors represent the expression profile of genes associated to a given state after the constructionof the map附加文件3：图S1。经质量过滤后，尾萼海膜（H. caudiculatum）与齿状海膜（H. dentatum）的Illumina Hiseq 100 bp双端测序读段的质量评分及准确率。直方图中分值≤20的低质量读段已被剔除；当测序仪读取的碱基准确率达99.9%时，对应读段的得分均高于30。 图S2。利用自组织映射（Self-Organizing Maps，SOM）对尾萼海膜与齿状海膜的基因平均距离进行训练的过程，展示了邻域收缩以覆盖获胜单元的效果，即当数据集中的向量达到最高相似度时的状态。 图S3。训练完成后，尾萼海膜与齿状海膜的码本向量（Codebook vectors）展示了具有最大邻域关联的差异表达基因簇。码本向量代表映射构建完成后与特定状态相关的基因表达谱。